Table 1

Key aspects of HexDiff and other algorithms. The table shows the knowledge used and the parameters required by the different algorithms.
Algorithm
 Knowledge Used
 Parameters
HexDiff
 CRM Locations
 Number of hexamers in Hd
Window size
Window score threshold
Ahab
 PWMs
 Window size
Free energy cutoff
Order of background model
Cluster Buster
 PWMs
 Motif score threshold
Gap parameter
Cluster score threshold
Residue abundance range
MSCAN
 PWMs
 Motif score threshold
Window size
Minimum hits
Maximum hits
MCAST
 PWMs
 Motif score threshold
Maximum allowed distance between adjacent hits
Pseudocount weight
LWF
 CRM Locations
 String length
Number of mismatches
Detection window size
Maximum number of channels
Channels equalized
Profile cutoff
Peak width cutoff
Smoothing window

Chan and Kibler BMC Bioinformatics 2005 6:262   doi:10.1186/1471-2105-6-262